The genetic contribution to a number of neurological disorders is thought to be complex in nature, disease risk being driven by a combination of "risk" alleles commonly present in the human genome. Recently the completion of stages I and II of the international Haplotype Map project and the availability of high-plex SNP assays has made genome wide assay of common genetic variability a realistic endeavor. We are applying genome wide association analysis usign ~500,000SNPs to disease and non-disease cohorts, these include cohorts with Parkinson's disease, Stroke, Amyotrophic Lateral Sclerosis and also neurologically normal controls, all from the NINDS funded neurogenetics repository. We have developed and implemented the necessary hardware and software infrastructure to store and manipulate the ~2 billion datapoints associated with these experiments. To data the experiments analysing Parkinson's disease are complete and have recently been published. THese data show that there is no single common genetic variant that has a major influence in risk for Parkinson's disease in the North American Caucasian population. We have posted these data on an open access website (www.coriell.org) for mining and augmentation by other interested researchers.